Cozumel is one of my favorite ports. The best excursion we have done there was the Royal Swim with Dolphins. We booked direct with Swim with Dolphins at Dolphin Discovery Cancun, Vallarta, Riviera Maya, Cozumel, Costa Maya, Mexico and the Caribbean it was expensive but a thrilling day we'll never forget.
Check out Cozumelinsider.com for lots of ideas re independent excursions.
We usually manage to shop a little downtown and try to always get to Pancho's backyard for lunch.
If you just want a beach day, there are lots of all inclusive beach clubs - Playa Mia, Nachi Cocum, Mr Sancho's you can go to.